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Marcel Dickmanns | 🌿❄️🔬 @madic.bsky.social · 23h

You can get MSAs directly from AlphaFold DB now (alphafold.ebi.ac.uk). I also missed the FoldSeek implementation, which lets you search for structurally similar proteins direktly.

This saves some clicking around. Neat!

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Malcolm White @mfwhite2.bsky.social · 6d

My pleasure @erinedoherty.bsky.social and @benmorehouse.bsky.social - for me this was the stand-out discovery of the last year in the field

Erin Doherty @erinedoherty.bsky.social · 6d

And thanks to @mfwhite2.bsky.social for this great perspective on both works! www.nature.com/articles/d41...

Bacteria use a decoy defence molecule to set a trap for viruses

Some bacterial-infecting viruses use ‘sponges’ to mop up defence molecules, but bacteria can fight back by responding when a sponge captures decoy molecules.

www.nature.com

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Ben Morehouse @benmorehouse.bsky.social · 6d

Our story describing the Panoptes bacterial immune defense system is now finally peer-reviewed and published today! www.nature.com/articles/s41...

The Panoptes system uses decoy cyclic nucleotides to defend against phage - Nature

The Panoptes antiphage system defends bacteria by detecting phage-encoded counter-defences that sequester cyclic nucleotide signals, triggering membrane disruption and highlighting a broader strategy of sensing immune evasion through second-messenger surveillance.

www.nature.com

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Ben Adler @benadler.bsky.social · 6d

Today in @nature.com , we highlight how a cousin of CRISPR-Cas10, mCpol, establishes an evolutionary trap in anti-phage immune systems.

Check out @erinedoherty.bsky.social and my work from @doudna-lab.bsky.social lab here:
www.nature.com/articles/s41...

A miniature CRISPR–Cas10 enzyme confers immunity by inhibitory signalling - Nature

Panoptes, an anti-phage defence system against virus-mediated immune suppression, is revealed.

www.nature.com

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Emmanuele Severi @emmseveri.bsky.social · 8d

www.nature.com/articles/s41...

#phagesky #phage defence

Molecular mechanisms of CBASS phospholipase effector CapV mediated membrane disruption - Nature Communications

CBASS systems trigger bacterial suicide via membrane disruption. Here, authors show that effector CapV relocates to the cell pole upon sensing 3’3’-cGAMP, where it cleaves phospholipids and ruptures membranes, revealing a filament-dependent activation mechanism for antiviral defense

www.nature.com

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Bethany Brookshire @beebrookshire.bsky.social · 11d

In reporting this piece on the new trial for a Huntington's treatment, I was struck by one thing in particular:

The joy.

One of my sources wept for joy. He has spent his entire career studying this disease, he said it was the happiest day. www.sciencenews.org/article/hunt...

Huntington's progression slowed by experimental gene therapy

An experimental gene therapy slowed Huntington’s by up to 75 percent in a small clinical trial. While not a cure, it may give patients longer lives.

www.sciencenews.org

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Sarah Lempriere @sarahlempriere.bsky.social · 12d

I found this fascinating! Termites build and tend a fungal garden. www.science.org/doi/10.1126/...

Gardening strategies of termite farmers

Termites use microbe-infused soil to protect a fungal symbiont

www.science.org

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Kranzusch Lab @kranzuschlab.bsky.social · 12d

You’ve heard of ubiquitination, meet deazaguanylation: Doug Wassarman in our lab discovered phage defense pathways have co-opted Q nucleobase biosynthetic enzymes to catalyze a new form of protein conjugation chemistry @science.org

www.science.org/doi/10.1126/...

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Diego del Alamo @delalamo.xyz · 13d

Still boggles my mind that we can leave frameworks as-is and only edit CDRs and still reliably get nM binders. Complete opposite of what I would have expected given how hard it is to graft CDRs from one FW to another (such as humanizing mouse mAbs). First RFantibody and now this

Arc Institute @arcinstitute.org · 13d

In another preprint from the @brianhie.bsky.social Lab and @synbiogaolab.bsky.social, they introduce Germinal, a generative AI system for de novo antibody design.

Germinal produces functional nanobodies in just dozens of tests, making custom antibody design more accessible than ever before.

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Asaf Levy @asaflevylab.bsky.social · 14d

A recent cool preprint by John Whitney's lab on a new family of antibacterial proteins secreted by Gram-positive bacteria that enter and kill a broad spectrum of bacteria. Cell entry is receptor-independent and relies on cleavage by a co-secreted protease and the PMF.
www.biorxiv.org/content/10.1...

Proteolytically activated antibacterial toxins inhibit the growth of diverse Gram-positive bacteria

Many species of bacteria produce small-molecule antibiotics that enter and kill a wide range of competitor microbes. However, diffusible antibacterial proteins that share this broad-spectrum activity ...

www.biorxiv.org

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Martin Steinegger 🇺🇦 @martinsteinegger.bsky.social · 17d

MMseqs2-GPU sets new standards in single query search speed, allows near instant search of big databases, scales to multiple GPUs and is fast beyond VRAM. It enables ColabFold MSA generation in seconds and sub-second Foldseek search against AFDB50. 1/n
📄 www.nature.com/articles/s41...
💿 mmseqs.com

GPU-accelerated homology search with MMseqs2 - Nature Methods

Graphics processing unit-accelerated MMseqs2 offers tremendous speedups for homology retrieval from metagenomic databases, query-centered multiple sequence alignment generation for structure predictio...

www.nature.com

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Alexis Verger 🧬🧫🧪 @alexis-verger.cpesr.fr · 19d

De novo design of All-atom biomolecular interactions with RFdiffusion3 www.biorxiv.org/content/10.1...

De novo Design of All-atom Biomolecular Interactions with RFdiffusion3

Deep learning has accelerated protein design, but most existing methods are restricted to generating protein backbone coordinates and often neglect interactions with other biomolecules. We present RFd...

www.biorxiv.org

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Nature Methods @natmethods.nature.com · 19d

GPU-accelerated MMseqs2 offers tremendous speedup for homology retrieval, protein structure prediction with ColabFold, and protein structure search with Foldseek. @martinsteinegger.bsky.social @milot.bsky.social @machine.learning.bio

www.nature.com/articles/s41...

GPU-accelerated homology search with MMseqs2 - Nature Methods

Graphics processing unit-accelerated MMseqs2 offers tremendous speedups for homology retrieval from metagenomic databases, query-centered multiple sequence alignment generation for structure predictio...

www.nature.com

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Julius Brennecke @juliusbrennecke.bsky.social · 21d

PIWI clade Argonautes are essential for transposon silencing. Without them, animals are sterile due to massive transposon activity.

But how does piRNA-guided target interaction translate into silencing?

PhD student Júlia Portell Montserrat has an intriguing answer

www.cell.com/molecular-ce...

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bioRxiv Microbiology @biorxiv-microbiol.bsky.social · 22d

YprA family helicases provide the missing link between diverse prokaryotic immune systems https://www.biorxiv.org/content/10.1101/2025.09.15.676423v1

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Ofer Yizhar @oyiz.bsky.social · 25d

Excited to share our latest paper - now out in @science.org - we showed how oxytocin modulates maternally-directed behavior in young mice (P15).

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Sorek Lab @soreklab.bsky.social · 27d

Phage "satellites" that produce capsids but have no genes to produce tails have puzzled scientists for a long time. These are abundant as prophages in bacteria, but it was unclear how they can infect without tails

Now, Penadés & co show that they hijack tails from other phages. Incredible!

José R Penadés @jrpenades.bsky.social · 28d

Thrilled to share our two latest papers with the @tcostalab.bsky.social
lab! In the first, we uncover a new mechanism of satellite transfer: cf-PICIs hijack tails from diverse phages to spread across species.
@imperialcollegeldn.bsky.social
www.cell.com/cell/fulltex...

Chimeric infective particles expand species boundaries in phage-inducible chromosomal island mobilization

Capsid-forming PICIs (cf-PICIs) produce their own capsids and exploit phage tails from unrelated species to transfer their DNA across bacterial hosts. This tail piracy enables broad dissemination and ...

www.cell.com

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Jörg Vogel @jorg-vogel-lab.bsky.social · 27d

Looking for a new approach to studying or eliminating phages? Check out our study introducing anti-phage ASOs (antisense oligos) out in @Nature today. nature.com/articles/s4158…

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José Cerca @naturalselection.bsky.social · 28d

Cool preprint! 🚨

Lanternfish lack MHC I and functional MHC II — yet still produce antibodies! 🧬🐟

www.biorxiv.org/content/10.1...

The genome of the Glacier lanternfish shows loss of MHC I and II function and provides insight into evolution of lanternfish immune systems

Lanternfishes (Myctophidae) are one of the most abundant and species diverse orders inhabiting the mesopelagic zone. Exploitation of marine resources has recently attracted increased interest. It is t...

www.biorxiv.org

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Zamin Iqbal @zaminiqbal.bsky.social · 28d

Sometimes you meet absolutely incredible bioinfo-magicians.
It was a huge privilege when @shenwei356.bsky.social
joined our group for a year on an @embl.org sabbatical.
While here, he developed a new way of aligning to
millions of bacteria, called LexicMap 1/n
www.nature.com/articles/s41...

Efficient sequence alignment against millions of prokaryotic genomes with LexicMap - Nature Biotechnology

LexicMap uses a fixed set of probes to efficiently query gene sequences for fast and low-memory alignment.

www.nature.com

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José R Penadés @jrpenades.bsky.social · 28d

Thrilled to share our two latest papers with the @tcostalab.bsky.social
lab! In the first, we uncover a new mechanism of satellite transfer: cf-PICIs hijack tails from diverse phages to spread across species.
@imperialcollegeldn.bsky.social
www.cell.com/cell/fulltex...

Chimeric infective particles expand species boundaries in phage-inducible chromosomal island mobilization

Capsid-forming PICIs (cf-PICIs) produce their own capsids and exploit phage tails from unrelated species to transfer their DNA across bacterial hosts. This tail piracy enables broad dissemination and ...

www.cell.com

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Reposted by Sorek Lab

Patrick Bryant @patrickbryant1.bsky.social · 28d

Update: RareFold 🧬
Our AI framework for protein design with 29 noncanonical AAs now shows designed binders (linear + cyclic) are non-immunogenic in patient-derived assays — paving the way for safe next-gen peptide therapeutics.
👉https://www.biorxiv.org/content/10.1101/2025.05.19.654846v2

RareFold: Structure prediction and design of proteins with noncanonical amino acids

Protein structure prediction and design have traditionally been limited to the 20 canonicalamino acids. Expanding this space to include noncanonical amino acids (NCAAs) offers newopportunities for pro...

www.biorxiv.org

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Sorek Lab @soreklab.bsky.social · Sep 7

Harnessing the anti-phage defense system DarTG for single-base editing in human cells - an impressive method developed by Chase Beisel and colleagues

Constantinos Patinios @copabio.bsky.social · Sep 4

🚀 New publication alert! 🚀

We just published in @natbiotech.nature.com:
👉 Targeted DNA ADP-ribosylation triggers templated repair in bacteria and base mutagenesis in eukaryotes
doi.org/10.1038/s415...

Targeted DNA ADP-ribosylation triggers templated repair in bacteria and base mutagenesis in eukaryotes - Nature Biotechnology

Append editing of ADP-ribosyl to thymine is used for precise modifications in bacteria and eukaryotes.

doi.org

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Melanie Blokesch @mblokesch.bsky.social · Sep 6

Excited to share my latest review, now published in the Royal Society theme issue on ‘The ecology and evolution of bacterial immune systems' (available OA):

Defence systems encoded by core genomic islands of seventh pandemic Vibrio cholerae royalsocietypublishing.org/doi/10.1098/...

Defence systems encoded by core genomic islands of seventh pandemic Vibrio cholerae | Philosophical Transactions of the Royal Society B: Biological Sciences

Vibrio cholerae, the causative agent of cholera, has triggered seven pandemics, with the seventh pandemic emerging in 1961. The success of seventh pandemic El Tor (7PET) V. cholerae as a human pathogen is linked to its acquisition of mobile genetic ...

royalsocietypublishing.org

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Royal Society Publishing @royalsocietypublishing.org · Sep 5

A new theme issue of #PhilTransB examines the evolutionary history of bacterial immune systems, their modes of action, and the patterns how different bacterial immune systems are distributed across different ecosystems. Read: buff.ly/Z4qdxY1

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